[Bioperl-l] Minimal versions requirements/warnings for SearchIO text parsing?
muratem at eng.uah.edu
Fri Feb 17 17:45:30 UTC 2006
On Thu, 16 Feb 2006, Chris Fields wrote:
> I'm floating this to see what people think...
> I'm beginning to wonder, especially when I'm wading through the
> regex/parsing nightmare in SearchIO::blast, if we should either require a
> minimal BLAST version number for parsing to work in SearchIO::blast. I
> could add a '$self->throw("Requires BLAST v2.x.x")' or at least give a
> warning if the blast version number is below a minimal version, so at least
> people will know what the problem is (not us!).
> The regexes are really piling up, and the latest changes in blastn and
> tblastx will require adding a few more. I also think that this would help
> remind everybody running the latest Bioperl that there are also newer
> versions of BLAST. My current thought is to get it working for the latest
> text output from NCBI, check it against the last version of BLAST (v.
> 2.2.12, which, luckily, blastcl3 generates), and not worry too much about
> older ones.
> Any thoughts on this?
I could live with it. I think most of the world runs on NCBI or WUBLAST
and it's easy to download/update either of those.
Thanks for the effort. I use SearchIO a lot.
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign
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